This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. The primary N-C[unreadable] bond cleavage by electron capture dissociation (ECD) or electron transfer dissociation (ETD) of a multiply charged peptide ion produces an even electron c ion and an odd electron z+ ion, the latter of which contains a radical which may initiate secondary fragmentations. These secondary fragmentations are all charge remote fragmentations (CRFs), because they do not involve the direct participation of a charged site. Secondary fragment ions generated by CRFs can be very useful for peptide structural analysis, as demonstrated by the utility of w-ions in isomer differentiation, but their presence may also complicate the spectral interpretation. In this study, secondary fragmentation of several synthetic peptides was studied by both ECD and ETD. In ECD, in addition to c and z+ ion formations, charge remote fragmentations (CRF) of z+ ions were abundant, resulting in internal fragment formation or partial/entire side chain losses from amino acids, sometimes several residues away from the backbone cleavage site, and to some extent multiple side chain losses. These secondary cleavages were postulated to be initiated by hydrogen abstraction at the [unreadable]-, [unreadable]-, or [unreadable]-position of the amino acid side chain, after the initial backbone cleavage in ECD. In comparison, ETD generates fewer CRF fragments than ECD, possibly due to small energy deposition and stabilization of radicals in z+ ions by collisional cooling in ETD. This secondary cleavage study will facilitate ECD/ETD spectra interpretation, and help de novo sequencing and database searching. These results were published in a recent J. Am. Soc. Mass Spectrom. article.